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Protein-protein Interfaces

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

Affinity and Avidity

Affinity and Avidity

Protein Networks

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

Ligand Binding Sites

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

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Protein-Drug Binding: Determination Methods

Determining protein-drug binding can be achieved through indirect and direct methods, each providing valuable insights into the interaction between proteins and drugs.
Indirect methods involve isolating the bound drug from its free form in biological samples such as blood, serum, or plasma. These techniques aim to measure the percentage of drugs bound to proteins. Equilibrium dialysis is a commonly used method where the free drug concentration at equilibrium is measured by separating the bound...

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Updated: Aug 22, 2025

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

Binding affinity prediction for antibody-protein antigen complexes: A machine learning analysis based on interface

Yong Xiao Yang¹, Pan Wang², Bao Ting Zhu²

¹Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, China.

Journal of Molecular Graphics & Modelling

|November 10, 2022

Summary

New models accurately predict antibody-protein binding affinity, outperforming general methods. Area-based descriptors show slightly better predictive power than contact-based ones for antibody therapeutics design.

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Determination of High-affinity Antibody-antigen Binding Kinetics Using Four Biosensor Platforms

Determination of High-affinity Antibody-antigen Binding Kinetics Using Four Biosensor Platforms

Published on: April 17, 2017

Area of Science:

Biochemistry and Structural Biology
Immunology
Computational Biology

Background:

Antibodies are key protein therapeutics due to specific antigen binding.
Accurate prediction of antibody-antigen binding affinity is vital for therapeutic antibody design.
Existing protein-protein binding affinity models lack accuracy for antibody-antigen complexes.

Purpose of the Study:

Develop novel models for antibody-antigen binding affinity prediction.
Investigate the utility of area-based and contacts-based descriptors.
Compare new models against existing general and specific methods.

Main Methods:

Utilized area-based and contacts-based descriptors for model development.
Trained and evaluated models specific to antibody-antigen interfaces.
Compared performance against general protein-protein affinity models and a graph-based model (CSM-AB).

Main Results:

Area-based descriptors demonstrated slightly superior predictive power over contacts-based descriptors.
Newly developed antibody-specific models significantly outperformed general protein-protein affinity models.
The best area-based and contacts-based models surpassed the performance of the CSM-AB graph-based model.

Conclusions:

Novel models enhance the accuracy of antibody-antigen binding affinity prediction.
These models offer improved understanding of antibody-antigen interactions.
The developed models have practical applications in designing and screening antibody-based therapeutics.